The judicial system is declared by the United States constitution, but it isn't defined by it. The judicial system is defined by laws passed over time. Those laws establish the district and circuit (appeals) courts. Only the Supreme Court is actually mentioned by name in Article III of the US constitution:
The judicial Power of the United States, shall be vested in one supreme Court, and in such inferior Courts as the Congress may from time to time ordain and establish.
The "inferior Courts" are ordained and established by Congress. There are various limitations provided in Article III and the Bill of Rights, but subject to those, the inferior courts are Congress' to define.
The "Criminal Justice System" is more than just the judicial branch. It also includes law enforcement like the FBI (Federal Bureau of Investigation), ATF (Bureau of Alcohol, Tobacco, Firearms & Explosives), and Homeland Security. The Department of Justice is also part of the criminal justice system. Defense attorneys and the criminal code are also part of the criminal justice system.
The constitution mandates defense attorneys, but it doesn't mandate how they get paid nor how much. Law enforcement and prosecution are pretty much entirely a creation of Congress.
- Sept. 24, 1789: Congress establishes a Supreme Court, 13 district courts, three ad hoc circuit courts, and the position of Attorney General.
Subject to constitutional restrictions, Congress can change, reform, or even alter those if it wants. It can't abolish the Supreme Court, but it could certainly change things. For example, the Supreme Court used to only have five members but now has nine.
Beyond all that, even the constitutional requirements are subject to amendment by Congress. That would still require ratification by three quarters of the states but is otherwise part of the federal government.